Let's see...
Religion's a tough one - there's the case where you WANT to spread religion in our lands, where we WANT to spread religions to other lands, and where we DON'T WANT another religion spreading at home. Each is basically a different advisor - Domestic might decide where to spread at home, FA might decide where to spread abroad (as Open Borders are basically required to spread religion), and there's the Theocracy Religious civic, which prevents the spread of religion other than the state one. We could create a religion advisor (a High Priest?) or shunt it all to the President.
Given the need for city specialization, I also suggest getting rid of seperately-elected governors entirely, or at least clearly subordinating them to a nationally elected advisor. There's too much risk to chaos and other hi-jinks if governors get too independent and move away from a city's pre-determined specialized set-up.
In fact, what you could do is have a Domestic Minister, who is in charge of all the minutiae of cities (and who has to worry less about micro-management thanks to Civ4, anyway), and a seperate Minister of Development who plans out city placement, worker actions, and maybe civics and religion.